Changes to cellular DNA are often deleterious, leading to the development of malignant tumors. Alterations in cellular DNA can accumulate as point mutations, deletions, inversions, translocations or sequence amplification. Sequence amplification is particularly common and has been detected in as much as 34% of breast cancers. It is often associated with advanced disease and poor prognosis. Detection of amplified genes within tumors is vital to determining patient outlook and treatment course. Fluorescence in situ hybridization (FISH) is a powerful tool for detecting nucleic acids in morphologically intact cells, however, assay sensitivity continues to be a significant obstacle to widespread usage. Improved diagnostic methods are needed to understand cancer pathogenesis and determine proper therapeutic intervention. This Small Business Innovation Research Phase I project aims to develop a sensitive, rapid, reproducible and cost effective FISH assay for detecting gene amplification in cancer biopsies.